Conflicting results are quite common in nutrition. I think the key here is that JAMA believes fatty fish benefits the cardiovascular system but fish oil supplements do not. If I had to theorize, I'd chalk it up to association (people who eat fatty fish often eat pretty wholesome diets), absorption of the fats (vs supplements which must be taken with a high fat meal to be absorbed), and lower EPA/DHA content found in many fish oils.

http://pescience.com/
http://selectprotein.com/
The above is my own opinion and does not reflect the opinion of PES

Conflicting results are quite common in nutrition. I think the key here is that JAMA believes fatty fish benefits the cardiovascular system but fish oil supplements do not. If I had to theorize, I'd chalk it up to association (people who eat fatty fish often eat pretty wholesome diets), absorption of the fats (vs supplements which must be taken with a high fat meal to be absorbed), and lower EPA/DHA content found in many fish oils.

This is also called bias of compliance. People who follow their doctors recommendations for one thing will often follow it for everything. While those who do not follow it for one thing will likely not follow it for most suggestions (i.e.: not exercise, smoke, drink, etc.). Hence one of the major issues with observational epidemiology.

From Gary Taubes:

The Bias of Compliance
A still more subtle component of healthy-user bias has to be confronted. This is the compliance or adherer effect. Quite simply, people who comply with their doctors’ orders when given a prescription are different and healthier than people who don’t. This difference may be ultimately unquantifiable. The compliance effect is another plausible explanation for many of the beneficial associations that epidemiologists commonly report, which means this alone is a reason to wonder if much of what we hear about what constitutes a healthful diet and lifestyle is misconceived.
The lesson comes from an ambitious clinical trial called the Coronary Drug Project that set out in the 1970s to test whether any of five different drugs might prevent heart attacks. The subjects were some 8,500 middle-aged men with established heart problems. Two-thirds of them were randomly assigned to take one of the five drugs and the other third a placebo. Because one of the drugs, clofibrate, lowered cholesterol levels, the researchers had high hopes that it would ward off heart disease. But when the results were tabulated after five years, clofibrate showed no beneficial effect. The researchers then considered the possibility that clofibrate appeared to fail only because the subjects failed to faithfully take their prescriptions.
As it turned out, those men who said they took more than 80 percent of the pills prescribed fared substantially better than those who didn’t. Only 15 percent of these faithful “adherers” died, compared with almost 25 percent of what the project researchers called “poor adherers.” This might have been taken as reason to believe that clofibrate actually did cut heart-disease deaths almost by half, but then the researchers looked at those men who faithfully took their placebos. And those men, too, seemed to benefit from adhering closely to their prescription: only 15 percent of them died compared with 28 percent who were less conscientious. “So faithfully taking the placebo cuts the death rate by a factor of two,” says David Freedman, a professor of statistics at the University of California, Berkeley [who passed away, regrettably, in 2008]. “How can this be? Well, people who take their placebo regularly are just different than the others. The rest is a little speculative. Maybe they take better care of themselves in general. But this compliance effect is quite a big effect.”
The moral of the story, says Freedman, is that whenever epidemiologists compare people who faithfully engage in some activity with those who don’t—whether taking prescription pills or vitamins or exercising regularly or eating what they consider a healthful diet—the researchers need to account for this compliance effect or they will most likely infer the wrong answer. They’ll conclude that this behavior, whatever it is, prevents disease and saves lives, when all they’re really doing is comparing two different types of people who are, in effect, incomparable.
This phenomenon is a particularly compelling explanation for why the Nurses’ Health Study and other cohort studies saw a benefit of H.R.T. [hormone replacement therapy, one subject of the article] in current users of the drugs, but not necessarily in past users. By distinguishing among women who never used H.R.T., those who used it but then stopped and current users (who were the only ones for which a consistent benefit appeared), these observational studies may have inadvertently focused their attention specifically on, as Jerry Avorn says, the “Girl Scouts in the group, the compliant ongoing users, who are probably doing a lot of other preventive things as well.”

Study was based on just 1 gram of fish oil and low epa/dha. So it's actually worthless information to me because I don't waste my time with low EPA/DHA and take way more than just 1 gram a day.

I guess you were reading my mind... although I thought the average was 1.5 grams (still not appropriate for most).

There's also more than one type of fish oil. Typically, in omega-3 intervention studies, subjects take pills containing a near-equal mixture of two fats, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA)—but some research suggests that in certain situations and for certain outcomes, one may be better than the other. For instance, a 2011 meta-analysis concluded that fish oil capsules don't help treat depression, but a group of British and Norwegian researchers challenged these findings, citing evidence that pills containing at least 60 percent EPA do seem to provide mood benefits. Another controversial question is whether the omega-3 dose is important in and of itself or whether the ratio of omega-3 to omega-6 fats one consumes is more important. (Although omega-6 fats are important for survival, Americans tend to consume far more of these fats than they need.)

For those that understand statistics, the authors used P value of 0.006 corrected for multiple comparisons without clear details or citation for the rationale. If the authors had used the standard criterion (P value of 0.05) or would have been more transparent as to why they used the stricter criterion, then the conclusion would have been easier to interpret. Unfortunately, this is a meta-analysis too which inherently harbors problems.

Do we know how many in the omega-3 groups were consistently taking omega-3s? Is there documentation about how much was taken specifically by those who had cardiovascular events and for how long? And do we know if the research subjects took omega-3 supplements or ate fatty fish regularly or sporadically? Do we know if the rest of their diet was healthy or not? Do we know how many were seriously ill with heart disease or another illness long before they began taking the omega-3s?

It turns out, on closer look, the patients studied only took an average of .05 ounces of omega-3 a day for an average of two years -- some for a year or less. There's no documentation about the formulation of various supplements (including potency, freshness) which most likely varied from trial to trial, too.

If you look at some of the specific studies used in the JAMA analysis that did use standard amounts of omega-3s, there's evidence they helped people with chronic heart failure. What's more, taking omega-3s was associated with reducing triglycerides, fats known to raise the risk of heart attacks and strokes. So, if the new study had analyzed patients for five or ten years, would this drop in triglycerides have lowered cardiovascular disease risk?

No one knows.

Unfortunately, the sloppy reporting of the new JAMA study was slanted toward easy, misleading headlines that pushed the idea the research was an end-all answer to whether omega-3s benefit health. Numerous news stories implied or flat out said that omega-3 supplements are a waste of money.

This is a ridiculous conclusion. Even if there were absolute proof omega-3s don't help your heart, a simple search of the U.S. National Library of Medicine reveals countless studies showing benefits of omega-3s to health -- including cancer prevention, possible prevention of lupus and the alleviation of depression.

Finally, whereas the recent JAMA analysis concluded that fish oil has no effect on cardiovascular outcomes, the researchers did find that omega-3s reduced the risk of cardiac death by 10 percent, an effect that was statistically significant (having a "p value" of 0.01). The researchers did not report the finding in their conclusions because they subsequently modified their statistical calculations to account for the fact that they had used the same data set to ask a number of different "exploratory" questions: In this case, does fish oil prevent heart attacks? Strokes? What about sudden cardiac death? The team wanted to tighten their definition of statistical significance to account for the fact that the more questions one asks, the more likely one is to get a positive result by chance. Still, Mozaffarian says, "if you combine all the data and look only at cardiac death, there is a statistically significant benefit. A 10 percent reduction in the number-one cause of death in both men and women in the U.S. is a big deal."

So, should you take fish oil pills or not? Most researchers agree that oily fish such as salmon and mackerel are far better way to get your fill of good fats. Many of the early, promising studies on omega-3s involved fish rather than fish oil pills (in one, men who were advised to eat fish were 29 percent less likely to die in the two years following a heart attack than men who were not), and a 2010 study by Columbia University scientists reported that following a Mediterranean diet—which, among other things, is rich in fatty fish—reduces the risk of Alzheimer's disease by 34 percent. Not only may people be benefiting from the omega-3 fatty acids in fish, but the fish may be displacing such foods as hamburgers and quiche from the diet, both high in saturated fat.

At the end of the day...my recommendations for fatty acids (previously posted) stand as far as I am concerned.